Evaluate gene sets identified by SDAN
Wei Sun
2024-07-12
Setup
Check enrichment of gene sets
Read in gene info and gene set assignments
cell_type_name = "CD8T"
file_tag = sprintf("%s_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 15.00 19.75 20.00 20.00 21.00 22.00## [1] 40## [1] 15 16 18 19 19 19 19 19 19 19 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
## [26] 20 21 21 21 21 21 21 21 21 21 21 22 22 22 22## [1] 800Find gene symbols
Find gene symbols from bioMart.
All the gene symbols that can be found in bioMart are
consistent with what we have. So no need to run it.
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"),
filters = "external_gene_name",
values = assayed_genes,
mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]
table(assayed_genes %in% gene_BM$external_gene_name)
t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]
table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]Find gene symbols using the alias2Symbol function from
limma.
a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "C7orf55"
## [1] "FMC1-LUC7L2" "FMC1"
## [1] "MARS"
## [1] "MARS1" "SLA2"
## [1] "QARS"
## [1] "EPRS1" "QARS1"
## [1] "APITD1"
## [1] "CENPS-CORT" "CENPS"
## [1] "HIST1H2BC"
## [1] "H2BC5" "H2BC4"##
## FALSE TRUE
## 1120 139##
## FALSE TRUE <NA>
## 71 1049 139gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: ZNRD1 POLR1H
## 2: C2orf43 LDAH
## 3: FAM45A DENND10
## 4: MTERF MTERF1
## 5: NARG2 ICE2
## 6: C6orf203 MTRES1
## 7: HRSP12 RIDA
## 8: FOPNL CEP20
## 9: WARS WARS1
## 10: LINS LINS1
## 11: RRNAD1 METTL25B
## 12: FAM122B PABIR2
## 13: WDYHV1 NTAQ1
## 14: HIST1H2BD H2BC5
## 15: AGPAT6 GPAT4
## 16: C1orf123 CZIB
## 17: KIAA1841 SANBR
## 18: C2orf44 WDCP
## 19: TMEM155 SMIM43
## 20: C7orf55 FMC1-LUC7L2
## 21: C9orf89 CARD19
## 22: C11orf82 DDIAS
## 23: XRCC6BP1 ATP23
## 24: MARS MARS1
## 25: C19orf55 PROSER3
## 26: HIST1H2AE H2AC8
## 27: QARS EPRS1
## 28: APITD1 CENPS-CORT
## 29: CCDC101 SGF29
## 30: PDDC1 GATD1
## 31: EFCAB4A CRACR2B
## 32: EIF2S3L EIF2S3B
## 33: HIST1H2BC H2BC5
## 34: WRB GET1
## 35: TMEM194B NEMP2
## 36: HIST1H4C H4C3
## 37: HIST1H4J H4C11
## 38: ZNF720 KRBOX5
## 39: HIST1H2BH H2BC9
## 40: FAM49A CYRIA
## 41: TTC37 SKIC3
## 42: C1orf85 GLMP
## 43: C9orf114 SPOUT1
## 44: HIST2H2AA4 H2AC19
## 45: HIST2H2BF H2BC18
## 46: C10orf128 TMEM273
## 47: TCTEX1D2 DYNLT2B
## 48: C17orf89 NDUFAF8
## 49: PHBP3 PHB1P3
## 50: SEPT7P7 SEPTIN7P7
## 51: LINC00493 SMIM26
## 52: HIST1H2BN H2BC15
## 53: ATP5J2 ATP5MF
## 54: AKAP2 PALM2AKAP2
## 55: WDR65 CFAP57
## 56: SRP14-AS1 SRP14-DT
## 57: CTC-436P18.1 SMIM15-AS1
## 58: HIST1H3G H3C8
## 59: EFTUD1P1 EFL1P1
## 60: ATP5A1P3 ATP5F1AP3
## 61: CCDC109B MCUB
## 62: C1orf63 RSRP1
## 63: TMEM66 SARAF
## 64: PCNXL2 PCNX2
## 65: ACRC GCNA
## 66: AMICA1 JAML
## 67: PRMT10 PRMT9
## 68: FAM102A EEIG1
## 69: SELM SELENOM
## 70: NBPF16 NBPF15
## 71: RPL9P9 RPL9P8
## sym_in_data sym_limmagene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma), gene_symbol := sym_limma]
dim(gene_info)## [1] 1259 3## sym_in_data sym_limma gene_symbol
## 1: C1orf112 C1orf112 C1orf112
## 2: MAD1L1 MAD1L1 MAD1L1
## 3: ICA1 ICA1 ICA1
## 4: NDUFAF7 NDUFAF7 NDUFAF7
## 5: ST7 ST7 ST7## t1
## 1 2
## 1255 2## sym_in_data sym_limma gene_symbol
## 1: HIST1H2BD H2BC5 H2BC5
## 2: HIST1H2BC H2BC5 H2BC5
## 3: RPL9P8 RPL9P8 RPL9P8
## 4: RPL9P9 RPL9P8 RPL9P8Prepare gene set information
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
gmtfile[["immune"]] = "../Annotation/c7.all.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp" "immune"## reactome go_bp immune
## 1692 7647 5219Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0
##
## $immune
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5 162 193 197 199 199 200 200 200 200 1992Conduct enrichment analysis
## [1] 1259 3## sym_in_data sym_limma gene_symbol
## 1: C1orf112 C1orf112 C1orf112
## 2: MAD1L1 MAD1L1 MAD1L1max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info$sym_in_data %in% gene_sets[[k]]
names(genes) = gene_info$gene_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol")
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.05)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=120)
goseq_res[[set_k]][[k1]] = res1
}
}
}## [1] 1
## [1] "MRPS33" "MTFMT" "CPD" "CUL9" "CCR2"
## [6] "PARP2" "C11orf1" "C7orf55" "GLB1" "ETFDH"
## [11] "MRPL48" "HIST1H2BC" "ZNF765" "TTC37" "HIST2H2AA4"
## [16] "HIST1H2BN"
## [1] 2
## [1] "PTP4A1" "FAHD2A" "MYB" "DTD2"
## [5] "DPH6" "NARF" "ZBTB39" "FBXO22"
## [9] "BOLA1" "RP11-383G10.3" "UBA52P6" "RP11-365H23.1"
## [13] "RPS27AP2" "ADH5P4" "PTGES3P1" "AC007041.2"
## [17] "RP11-382J24.2" "LEF1" "SIK1" "MTND4P12"
## [21] "RP11-727F15.9"
## [1] 3
## [1] "REC8" "DUS4L" "GALK1" "IFNG" "GNPTAB"
## [6] "MCM9" "GORASP1" "STK25" "STYXL1" "TMEM218"
## [11] "LRRC28" "SPATA13" "EDARADD" "PIK3IP1" "ARRDC2"
## [16] "SLC38A2" "AMICA1" "PFKFB3" "RBKS" "RP11-44N11.1"
## [1] 4
## [1] "SH3BP2" "SNX14" "TAF10" "B2M" "AFMID" "TMSB4X" "IFRD1"
## [8] "RGPD5" "CD44" "ARHGEF1" "STK17B" "RGCC" "EGR1" "FOSB"
## [15] "JUND" "BTG2" "CXCR5" "TTC3" "RGPD6" "MALAT1"
## [1] 5
## [1] "CD200" "RP3-324O17.4" "ZNF419" "ZNF684"
## [5] "IL10" "RHEBL1" "C19orf55" "ZNF93"
## [9] "PIGW" "C2orf76" "ANAPC10P1" "RSC1A1"
## [13] "RP11-247I13.6" "CTC-338M12.4" "RP11-262H14.3" "CTB-4E7.1"
## [17] "HMGB1P24" "AP000462.1" "RP11-307P22.1" "RP11-638I2.10"
## [21] "RP11-1012A1.7" "TRAV30"
## [1] 6
## [1] "PIM2" "IFI6" "USF1" "IFI27"
## [5] "RP11-23P13.6" "ZNF80" "EIF2S3L" "ABHD16B"
## [9] "ZNF649" "SGMS1" "TRBV20-1" "TRAV19"
## [13] "TRAV24" "RP4-800M22.1" "RPS11P5" "RP11-288E14.2"
## [17] "AC144530.1" "RP11-693N9.2" "EEF1A1P10" "RP11-705C15.5"
## [1] 7
## [1] "VPS37A" "THAP2" "TRAV16" "TRAV21"
## [5] "RP1-102E24.1" "RP3-340B19.5" "RP11-2F9.3" "RPL19P12"
## [9] "RP11-270C12.3" "PGAM4" "GS1-124K5.2" "RPL19P21"
## [13] "AC090804.1" "RP11-446E9.1" "CTD-2301A4.3" "CTB-33G10.1"
## [17] "RNF138P1" "MIR146A" "HSPA8P5" "RP11-511H9.4"
## [21] "RP11-304L19.5"
## [1] 8
## [1] "CPQ" "RCAN3" "C1orf63" "NBPF14"
## [5] "PCNXL2" "NBPF10" "AC018720.10" "LDOC1"
## [9] "TSHZ2" "NBPF16" "HLA-J" "AC084018.1"
## [13] "HCG4P5" "RPL10P3" "HLA-W" "LINC00674"
## [17] "PSMD6-AS2" "ZNF10" "SLC7A5P1" "CTD-2017D11.1"
## [1] 9
## [1] "RGS1" "GMPR2" "PRMT7" "TRANK1"
## [5] "TRAPPC11" "CXCR6" "COA3" "CMC1"
## [9] "MT1X" "CCL3L1" "TECPR1" "TRGC2"
## [13] "PET100" "PVT1" "CCL3L3" "RP11-345J4.6"
## [17] "EIF1" "RP11-572P18.1" "RPS3AP6" "CTD-2031P19.4"
## [1] 10
## [1] "ZNF85" "MTHFS" "SCRN2" "FAM122B" "TMEM155"
## [6] "LAIR2" "ZBTB8OS" "ASB8" "GEN1" "ARHGAP11B"
## [11] "TMEM194B" "HIST1H4C" "ZNF28" "CRYGS" "AC098614.2"
## [16] "BDH2P1" "GAPDHP2" "RP11-265N6.2" "NPAT" "TCEAL3"
## [21] "TMEM9B-AS1"
## [1] 11
## [1] "REXO1" "POP4" "C3orf14" "GALE" "TMEM214" "CCDC77" "CKS2"
## [8] "UROD" "CCNB1" "FHOD1" "RPP30" "MPPE1" "GALK2" "CCNB2"
## [15] "POP5" "RUFY2" "MYCBP" "KIR3DL2"
## [1] 12
## [1] "CDKN3" "TIMM9" "TXNDC17" "FIGNL1" "TIMM10"
## [6] "TROAP" "GEMIN6" "NDUFAF6" "CCDC28B" "PAQR4"
## [11] "C11orf82" "ZFYVE19" "UBE2C" "TYMS" "SESTD1"
## [16] "NCKIPSD" "MDP1" "HIST1H3G" "PMF1-BGLAP"
## [1] 13
## [1] "SLAMF8" "TNFAIP8L2" "EFCAB7" "RPSAP54"
## [5] "RP11-12M9.4" "RPS19P1" "CALM2P3" "ARPC3P1"
## [9] "PRDX3P1" "SKP1P1" "AC093391.2" "AP000476.1"
## [13] "RPSAP4" "RPS19P3" "AC018462.3" "GAPDHP60"
## [17] "RP11-402J6.3" "RP13-638C3.4" "RP11-209D14.4" "CTB-52I2.4"
## [21] "RP11-282O18.6"
## [1] 14
## [1] "GCFC2" "MFAP3" "CD84" "CDKL1" "XAF1"
## [6] "MFSD9" "CASP1" "TMEM19" "TATDN1" "FCRL3"
## [11] "ZNF720" "SH2D1B" "CPT1B" "UBXN2B" "LINC00426"
## [16] "RBBP4P1" "SNORD3A" "AC024592.12" "MS4A1" "PLA2G4B"
## [1] 15
## [1] "GPN2" "ZBED2" "PLA2G6" "TXK"
## [5] "CLDND1" "MAN1C1" "RASGEF1B" "FRMD4A"
## [9] "POLR2J3" "YPEL2" "DENND5A" "RP11-514P8.6"
## [13] "RP11-91K8.4" "MTND1P23" "ACTBP12" "RP1-187B23.1"
## [17] "LINC00944" "RP11-335G20.7" "RP11-1000B6.3" "KCNQ1OT1"
## [1] 16
## [1] "RNF10" "BCL3" "DERL2" "MBNL3"
## [5] "FMR1" "METTL8" "KATNBL1" "TPGS2"
## [9] "TMOD3" "LINS" "LPP" "KBTBD2"
## [13] "KATNA1" "C17orf89" "PPIL3" "ATP5J2"
## [17] "RP11-386G11.10" "CLK1" "ABLIM1" "TC2N"
## [1] 17
## [1] "MED24" "TM7SF3" "POLD3" "DUSP12" "PLA2G15" "RASSF4" "NR2C1"
## [8] "NQO2" "ASNSD1" "TBCD" "UCK2" "PPP4R1" "NTAN1" "PPARA"
## [15] "ZNF511" "TRGV10" "TREX1" "MRPL33" "ABHD14A" "GGT7"
## [1] 18
## [1] "DYRK4" "NSMAF" "NHP2P1" "IL18RAP"
## [5] "FAM45A" "MTERF" "NUDT7" "AMDHD2"
## [9] "NAALADL1" "EFCAB4A" "WDR53" "ZNF749"
## [13] "TRGV5" "RP11-247I13.3" "RP11-119F19.2" "HNRNPKP2"
## [17] "PA2G4P4" "EEF1A1P14" "TRGV7" "KB-1507C5.2"
## [21] "TRAV1-2" "CTB-31O20.3"
## [1] 19
## [1] "PUS7L" "KHDC1" "SFR1" "KIAA1841" "LRRC45" "NME6"
## [7] "SWI5" "ZNF613" "LCORL" "LRTOMT" "CCDC30" "ENTPD5"
## [13] "METTL6" "MYL5" "PIN4P1" "SAPCD1" "GK3P" "RAB1C"
## [19] "GOT2P3" "ZEB1-AS1" "RPL13P5"
## [1] 20
## [1] "PRSS23" "AMFR" "MRPL55" "RPS17" "TNF" "PPP2R5C" "RPL34"
## [8] "RPS12" "RPL21" "RPL5" "BTG1" "PDCD4" "ZFP36L2" "RPL9"
## [15] "RPS18"
## [1] 21
## [1] "CCL3" "GLT8D1" "TBPL1" "FAR2" "GZMB" "MAN2B1"
## [7] "SLC12A4" "MT2A" "ANXA1" "IRF4" "GCHFR" "GTF2A2"
## [13] "C1orf123" "EXTL2" "METTL18" "PRF1" "NCR3" "UBE2D3P2"
## [19] "NR4A2" "CD55"
## [1] 22
## [1] "MAP3K13" "ZNF268" "FAH" "EGR2"
## [5] "TMSB15B" "MEI1" "ADCK5" "SNHG11"
## [9] "ZNF257" "ZNF525" "LYPLA1P3" "ZNF826P"
## [13] "LINC00493" "SNRPEP4" "FAM200B" "RP11-552M11.4"
## [17] "SRP14-AS1" "TPM3P6" "USP30-AS1" "RP11-1094M14.7"
## [21] "RIMKLB"
## [1] 23
## [1] "OCEL1" "DHDDS" "PGPEP1" "RRNAD1" "RNF25"
## [6] "SLC39A13" "RPSAP47" "ZNF544" "TRAV8-2" "RP4-694B14.5"
## [11] "DNASE1" "PTGES3P2" "CCT8P1" "RP11-350G8.3" "SEPT7P7"
## [16] "RP11-782C8.1" "TSEN15P1" "FAM21FP" "ETF1P2" "SF3A3P2"
## [21] "RP4-739H11.4"
## [1] 24
## [1] "STAU2" "P2RX5" "ERGIC2" "DHPS" "THOC5" "DDX49" "SRM"
## [8] "IMP4" "MAP3K6" "LIMD1" "GLUD1" "CXXC1" "MITD1" "MARS"
## [15] "NT5DC1" "DUSP28" "PIK3R4" "TNRC6C" "LMO7" "PPP1R10"
## [1] 25
## [1] "CRTAM" "HAVCR1" "TNFSF10" "PTGER2" "IFI44L"
## [6] "IFI44" "APH1B" "SPON2" "MT1E" "HOPX"
## [11] "TRBV9" "TRAV13-1" "MIR155HG" "AC092580.4" "RN7SL749P"
## [16] "AC005329.7" "RNU1-125P" "AC006483.1" "MIR142" "AC006129.4"
## [1] 26
## [1] "NOP16" "WDR3" "GTPBP10" "NOP2" "DKC1" "MTO1"
## [7] "BCAS3" "PELP1" "UTP23" "PHAX" "ZFP62" "ZNF431"
## [13] "ZNF770" "C9orf114" "ZBTB48" "RASGRF2" "SGSM2" "FAM102A"
## [19] "DNHD1"
## [1] 27
## [1] "C14orf93" "MS4A6A" "TMEM138" "TRPT1"
## [5] "GSTM4" "TRDV1" "RP13-383K5.4" "CD27-AS1"
## [9] "TSTD1" "RNU2-2P" "AC012318.3" "RP11-773D16.1"
## [13] "RP4-742C19.12" "TRGV2" "MAPKAPK5-AS1" "AC104820.2"
## [17] "LINC00484" "RP11-305L7.3" "RP11-416A17.6" "CTD-2521M24.9"
## [1] 28
## [1] "TNFRSF9" "PON2" "KLRB1" "TEP1" "ACTR10" "KLRC1"
## [7] "BORA" "SPPL2A" "PANK4" "MGAT4B" "FCGR3B" "SLC38A9"
## [13] "WRB" "CCL4L2" "FCGR3A" "MSH5" "CCL4L1" "KLRC2"
## [19] "TCTEX1D2"
## [1] 29
## [1] "PECR" "XCL1" "XCL2" "CX3CR1" "GTSF1"
## [6] "ZNF683" "FCRL6" "C10orf128" "TRBV4-2" "TRAV14DV4"
## [11] "TRAV29DV5" "TRAV35" "KANSL1-AS1" "RP1-182O16.1" "PATL2"
## [16] "AKAP2" "RPL37P23" "RP11-81H14.2" "AC139149.1" "TPMTP1"
## [21] "LUZP6"
## [1] 30
## [1] "ZNRD1" "MICALL1" "CAPN15" "POLR2I" "CD86" "MTFR1L" "IFIT3"
## [8] "IFIT2" "UXT" "HRSP12" "RSAD2" "CLSTN3" "KSR1" "MED11"
## [15] "POLR2H" "IL15" "TMEM107" "IFIT1" "TRGV3"
## [1] 31
## [1] "MDGA1" "CDCA7L" "ZNF816" "RPS12P26"
## [5] "TCF7" "CCR7" "C1orf162" "LDLRAP1"
## [9] "PLXDC1" "FILIP1L" "TMEM150A" "CD248"
## [13] "POU6F1" "TRABD2A" "MIR4461" "CTD-3092A11.1"
## [17] "RP11-632K20.7" "CHRM3-AS2" "RP11-285F7.2" "WHAMMP2"
## [21] "RP1-313I6.12"
## [1] 32
## [1] "PTPN18" "TIPIN" "NSMCE4A" "NCOA7"
## [5] "AHI1" "APTX" "RNF121" "HIRIP3"
## [9] "MFSD6" "ALG8" "PRIMPOL" "CTSB"
## [13] "GNGT2" "KIR3DL1" "TBCA" "MZT2A"
## [17] "DALRD3" "TNFRSF18" "KIR2DS4" "RP11-271C24.3"
## [1] 33
## [1] "PDE6B" "ZNF678" "RP4-728D4.2" "RP11-493L12.6"
## [5] "DGKA" "NEK1" "FBXO32" "EPB41"
## [9] "PLGLB1" "RPS26P6" "RPS3AP26" "RPL9P8"
## [13] "RPL3P4" "AP001468.1" "RPL9P9" "RPL9P7"
## [17] "ATP1B3-AS1" "RP13-488H8.1" "RP11-320M16.1"
## [1] 34
## [1] "PMM1" "TFDP2" "C2orf43" "CCRL2"
## [5] "NARG2" "TMEM241" "SLC2A8" "SLC35A5"
## [9] "FUOM" "DRAM2" "LZTFL1" "TRIM68"
## [13] "TMEM134" "SMIM19" "SLC9A9" "TRDC"
## [17] "RP11-254B13.4" "BHLHE40-AS1" "RP11-844P9.3" "RP11-265N6.3"
## [21] "MIR3615" "RP11-686D22.10"
## [1] 35
## [1] "CHI3L2" "NT5C2" "WARS" "TMPRSS3"
## [5] "DNAJC18" "PSMG1" "FAM49A" "PSMA6P1"
## [9] "AC009403.2" "RNU2-63P" "CDC42P1" "AC002331.1"
## [13] "RP11-32B5.1" "RP3-395M20.8" "RN7SL56P" "GMPSP1"
## [17] "RPPH1" "MIR3661" "AL161784.1" "CTD-3214H19.4"
## [21] "CTD-2545M3.2" "RP11-297D21.4"
## [1] 36
## [1] "C9orf89" "CMAHP" "RASGRP2" "MGAT4A" "HECA"
## [6] "NR4A3" "FAM117B" "PLAC8" "ACRC" "TIPARP"
## [11] "PRMT10" "CHD2" "PLK3" "ZBTB20" "ANKRD37"
## [16] "SELL" "AC021593.1" "LTB" "RP11-747H7.3" "RP11-434H6.7"
## [1] 37
## [1] "NDUFAF7" "SMG6" "IL4R" "USP48" "WDR7"
## [6] "UTP6" "EMG1" "L3HYPDH" "DEF8" "SEC24D"
## [11] "AGPAT6" "BAP1" "GNG4" "CHAMP1" "MBD5"
## [16] "CATSPER2P1" "FOXP1" "DHRS3" "SATB1"
## [1] 38
## [1] "RABGAP1" "NTHL1" "GBA2" "DHRS12" "LIN7B"
## [6] "ILVBL" "LIG1" "SNX8" "PRR4" "RCOR3"
## [11] "NUP85" "CHTF18" "FOPNL" "TTLL4" "COG5"
## [16] "KNTC1" "IFRD2" "RP11-33B1.1" "PMEPA1" "MPP7"
## [1] 39
## [1] "WDR13" "GABPB1" "SLC11A2" "LOXL3" "FANCL"
## [6] "ID3" "IRF8" "PMAIP1" "PLIN2" "CETN3"
## [11] "MTHFD2L" "NFU1" "PCGF5" "CADM1" "BTLA"
## [16] "TDRD7" "HIST1H4J" "FANCG" "AL358333.1"
## [1] 40
## [1] "CAPN12" "TRAV12-2" "PLXND1" "APBA2" "UAP1"
## [6] "TMEM66" "AOAH" "CDC42EP3" "ZNF589" "NPIPB3"
## [11] "NPIPB4" "RPS26" "FAM169A" "KLRK1" "MTND2P28"
## [16] "CTD-2328D6.1" "RPL41" "NPIPB5" "MTATP6P1" "QRSL1P3"
## [21] "RP11-51J9.5"
for(n1 in names(goseq_res)){
k = as.numeric(gsub("set_", "", n1))
print(n1)
print(gene_sets[[k]])
print(goseq_res[[n1]])
}## [1] "set_3"
## [1] "REC8" "DUS4L" "GALK1" "IFNG" "GNPTAB"
## [6] "MCM9" "GORASP1" "STK25" "STYXL1" "TMEM218"
## [11] "LRRC28" "SPATA13" "EDARADD" "PIK3IP1" "ARRDC2"
## [16] "SLC38A2" "AMICA1" "PFKFB3" "RBKS" "RP11-44N11.1"
## $go_bp
## category over_represented_pvalue
## 241 carbohydrate phosphorylation 6.272519e-07
## under_represented_pvalue numDEInCat numInCat FDR
## 241 1 4 5 0.002563578
##
## [1] "set_11"
## [1] "REXO1" "POP4" "C3orf14" "GALE" "TMEM214" "CCDC77" "CKS2"
## [8] "UROD" "CCNB1" "FHOD1" "RPP30" "MPPE1" "GALK2" "CCNB2"
## [15] "POP5" "RUFY2" "MYCBP" "KIR3DL2"
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 3987 trna 5 leader removal 8.087298e-06 1.0000000
## 3698 rna 5 end processing 2.995770e-05 0.9999999
## 3699 rna capping 2.995770e-05 0.9999999
## 3986 trna 5 end processing 2.995770e-05 0.9999999
## numDEInCat numInCat FDR
## 3987 3 3 0.03060928
## 3698 3 4 0.03060928
## 3699 3 4 0.03060928
## 3986 3 4 0.03060928
##
## $immune
## category over_represented_pvalue
## 3317 gse36826 wt vs il1r ko skin staph aureus inf up 8.40456e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 3317 0.9999998 5 17 0.04285485
##
## [1] "set_20"
## [1] "PRSS23" "AMFR" "MRPL55" "RPS17" "TNF" "PPP2R5C" "RPL34"
## [8] "RPS12" "RPL21" "RPL5" "BTG1" "PDCD4" "ZFP36L2" "RPL9"
## [15] "RPS18"
## $reactome
## category
## 890 srp dependent cotranslational protein targeting to membrane
## 256 eukaryotic translation initiation
## 734 response of eif2ak4 gcn2 to amino acid deficiency
## 255 eukaryotic translation elongation
## 691 regulation of expression of slits and robos
## 547 nonsense mediated decay nmd
## 808 selenoamino acid metabolism
## 986 translation
## 117 cellular response to starvation
## 869 signaling by robo receptors
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 890 1.418360e-05 0.9999992 7 29
## 256 1.575643e-05 0.9999991 7 30
## 734 1.751556e-05 0.9999990 7 30
## 255 1.766013e-05 0.9999990 7 31
## 691 1.991804e-05 0.9999988 7 31
## 547 2.074074e-05 0.9999988 7 31
## 808 2.347818e-05 0.9999986 7 32
## 986 2.350223e-05 0.9999983 8 46
## 117 2.692313e-05 0.9999983 7 33
## 869 2.696435e-05 0.9999983 7 33
## FDR
## 890 0.002755757
## 256 0.002755757
## 734 0.002755757
## 255 0.002755757
## 691 0.002755757
## 547 0.002755757
## 808 0.002755757
## 986 0.002755757
## 117 0.002755757
## 869 0.002755757
##
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 515 cytoplasmic translation 1.573413e-06 0.9999999
## numDEInCat numInCat FDR
## 515 7 33 0.006430541
##
## $immune
## category over_represented_pvalue
## 1974 gse22886 naive tcell vs dc up 4.358409e-07
## under_represented_pvalue numDEInCat numInCat FDR
## 1974 1 7 33 0.002222353
##
## [1] "set_26"
## [1] "NOP16" "WDR3" "GTPBP10" "NOP2" "DKC1" "MTO1"
## [7] "BCAS3" "PELP1" "UTP23" "PHAX" "ZFP62" "ZNF431"
## [13] "ZNF770" "C9orf114" "ZBTB48" "RASGRF2" "SGSM2" "FAM102A"
## [19] "DNHD1"
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 3693 ribosome biogenesis 8.642201e-07 1.0000000
## 1442 ncrna processing 5.031860e-06 0.9999997
## numDEInCat numInCat FDR
## 3693 7 35 0.003532067
## 1442 7 42 0.010282606
##
## [1] "set_30"
## [1] "ZNRD1" "MICALL1" "CAPN15" "POLR2I" "CD86" "MTFR1L" "IFIT3"
## [8] "IFIT2" "UXT" "HRSP12" "RSAD2" "CLSTN3" "KSR1" "MED11"
## [15] "POLR2H" "IL15" "TMEM107" "IFIT1" "TRGV3"
## $immune
## category
## 5059 scherer pbmc apsv wetvax age 18 32yo 2 to 4dy up
## 2344 gse26030 th1 vs th17 day5 post polarization up
## 3498 gse37533 pparg1 foxp3 vs pparg2 foxp3 transduced cd4 tcell pioglitazone treated dn
## 5061 scherer pbmc apsv wetvax age 18 32yo 5 to 7dy up
## 1648 gse21360 primary vs quaternary memory cd8 tcell up
## 4652 gse7509 dc vs monocyte with fcgriib stim dn
## 4763 gse8835 cd4 vs cd8 tcell cll patient up
## 466 gse14000 unstim vs 16h lps dc translated rna dn
## 1452 gse19888 adenosine a3r inh vs act with inhibitor pretreatment in mast cell up
## 1317 gse18281 subcapsular vs central cortical region of thymus dn
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 5059 1.576970e-06 1.0000000 5 12
## 2344 3.135367e-06 0.9999999 6 24
## 3498 4.853328e-06 0.9999998 6 25
## 5061 2.606480e-05 0.9999985 6 34
## 1648 4.127326e-05 0.9999982 5 22
## 4652 5.214184e-05 0.9999976 5 23
## 4763 5.405585e-05 0.9999975 5 23
## 466 6.332070e-05 0.9999970 5 23
## 1452 7.653433e-05 0.9999961 5 25
## 1317 9.103684e-05 0.9999952 5 26
## FDR
## 5059 0.007993618
## 2344 0.007993618
## 3498 0.008249039
## 5061 0.033226104
## 1648 0.039375824
## 4652 0.039375824
## 4763 0.039375824
## 466 0.040359029
## 1452 0.042095927
## 1317 0.042095927
##
## [1] "set_34"
## [1] "PMM1" "TFDP2" "C2orf43" "CCRL2"
## [5] "NARG2" "TMEM241" "SLC2A8" "SLC35A5"
## [9] "FUOM" "DRAM2" "LZTFL1" "TRIM68"
## [13] "TMEM134" "SMIM19" "SLC9A9" "TRDC"
## [17] "RP11-254B13.4" "BHLHE40-AS1" "RP11-844P9.3" "RP11-265N6.3"
## [21] "MIR3615" "RP11-686D22.10"
## $immune
## category
## 4783 gse8921 unstim vs tlr1 2 stim monocyte 12h up
## 2532 gse2770 tgfb and il4 vs il4 treated act cd4 tcell 6h up
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4783 1.594931e-06 1.0000000 5 16
## 2532 4.743483e-06 0.9999999 5 19
## FDR
## 4783 0.008132555
## 2532 0.012093510Session information
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8958397 478.5 17067254 911.5 NA 17067254 911.5
## Vcells 19166084 146.3 58167881 443.8 65536 78485130 598.8## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0
## [2] GenomicFeatures_1.50.4
## [3] GenomicRanges_1.50.2
## [4] GenomeInfoDb_1.34.9
## [5] org.Hs.eg.db_3.16.0
## [6] AnnotationDbi_1.60.2
## [7] IRanges_2.32.0
## [8] S4Vectors_0.36.2
## [9] Biobase_2.58.0
## [10] BiocGenerics_0.44.0
## [11] goseq_1.50.0
## [12] geneLenDataBase_1.34.0
## [13] BiasedUrn_2.0.10
## [14] fgsea_1.24.0
## [15] biomaRt_2.54.1
## [16] limma_3.54.2
## [17] tidyr_1.3.0
## [18] ggpubr_0.6.0
## [19] ggplot2_3.4.2
## [20] data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-162 matrixStats_1.0.0
## [3] bitops_1.0-7 bit64_4.0.5
## [5] filelock_1.0.2 progress_1.2.2
## [7] httr_1.4.6 tools_4.2.3
## [9] backports_1.4.1 bslib_0.4.2
## [11] utf8_1.2.3 R6_2.5.1
## [13] mgcv_1.8-42 DBI_1.1.3
## [15] colorspace_2.1-0 withr_2.5.0
## [17] tidyselect_1.2.0 prettyunits_1.1.1
## [19] bit_4.0.5 curl_5.0.1
## [21] compiler_4.2.3 cli_3.6.1
## [23] xml2_1.3.4 DelayedArray_0.24.0
## [25] rtracklayer_1.58.0 sass_0.4.5
## [27] scales_1.2.1 rappdirs_0.3.3
## [29] Rsamtools_2.14.0 stringr_1.5.0
## [31] digest_0.6.31 rmarkdown_2.21
## [33] XVector_0.38.0 pkgconfig_2.0.3
## [35] htmltools_0.5.5 MatrixGenerics_1.10.0
## [37] dbplyr_2.3.2 fastmap_1.1.1
## [39] rlang_1.1.0 rstudioapi_0.14
## [41] RSQLite_2.3.1 BiocIO_1.8.0
## [43] jquerylib_0.1.4 generics_0.1.3
## [45] jsonlite_1.8.4 BiocParallel_1.32.6
## [47] dplyr_1.1.2 car_3.1-2
## [49] RCurl_1.98-1.12 magrittr_2.0.3
## [51] GO.db_3.16.0 GenomeInfoDbData_1.2.9
## [53] Matrix_1.6-4 Rcpp_1.0.10
## [55] munsell_0.5.0 fansi_1.0.4
## [57] abind_1.4-5 lifecycle_1.0.3
## [59] stringi_1.7.12 yaml_2.3.7
## [61] carData_3.0-5 SummarizedExperiment_1.28.0
## [63] zlibbioc_1.44.0 BiocFileCache_2.6.1
## [65] grid_4.2.3 blob_1.2.4
## [67] parallel_4.2.3 crayon_1.5.2
## [69] lattice_0.20-45 splines_4.2.3
## [71] Biostrings_2.66.0 cowplot_1.1.1
## [73] hms_1.1.3 KEGGREST_1.38.0
## [75] knitr_1.44 pillar_1.9.0
## [77] rjson_0.2.21 ggsignif_0.6.4
## [79] codetools_0.2-19 fastmatch_1.1-3
## [81] XML_3.99-0.14 glue_1.6.2
## [83] evaluate_0.20 png_0.1-8
## [85] vctrs_0.6.2 gtable_0.3.3
## [87] purrr_1.0.1 cachem_1.0.7
## [89] xfun_0.39 broom_1.0.4
## [91] restfulr_0.0.15 rstatix_0.7.2
## [93] tibble_3.2.1 GenomicAlignments_1.34.1
## [95] memoise_2.0.1